<p>The fractional quantum Hall effect (FQHE), discovered in 1982 in a two-dimensional electron system, has generated a wealth of successful theory and new concepts in condensed matter physics, but is still not fully understood. The possibility of having nonabelian quasiparticle statistics has recently attracted attention on purely theoretical grounds but also because of its potential applications in topologically protected quantum computing.</p><p>This thesis focuses on the quasiparticles using three different approaches. The first is an effective Chern-Simons theory description, where the noncommutativity imposed on the classical space variables captures the incompressibility. We propose a construction of the quasielectron and illustrate how many-body quantum effects are emulated by a classical noncommutative theory.</p><p>The second approach involves a study of quantum Hall states on a torus where one of the periods is taken to be almost zero. Characteristic quantum Hall properties survive in this limit in which they become very simple to understand. We illustrate this by giving a simple counting argument for degeneracy 2<i>n</i>^-1, pertinent to nonabelian statistics, in the presence of 2<i>n</i> quasiholes in the Moore-Read state and generalise this result to 2<i>n</i>-<i>k</i> quasiholes and <i>k </i>quasielectrons.</p><p>In the third approach, we study the topological nature of the degeneracy 2<i>n</i>^-1 by using a recently proposed analogy between the Moore-Read state and the two-dimensional spin-polarized p-wave BCS state. We study a version of this problem where one can use techniques developed in the context of high-<i>T</i>c superconductors to turn the vortex background into an effective gauge field in a Dirac equation. Topological arguments in the form of index theory gives the degeneracy 2<i>n</i>^-1 for 2<i>n</i> vortices.</p>

Condensed matter physics is a rapidly evolving field of research enriched with the synthesis of new materials exhibiting a bewildering variety of phenomena and advances in experimental techniques. Over the years, discoveries and innovations in electronic systems have emphasized the crucial role played by correlations among electrons behind many of the observed unusual properties and have posed serious challenges to the physics community by exposing the lack of well-controlled theoretical methods to study the class of materials known as strongly correlated electronic systems. In these systems, known theoretical techniques typically fail to capture the essential features of the many-body ground state and finite temperature properties of the systems as typical electronic interaction energies are of order of or larger than the kinetic energies. The study of strongly correlated electronic systems went through a revolution in the 1980s and 1990s after the discovery of superconductivity inorganic compounds, in heavy fermion systems and ultimately in copper oxides, referred to as cuprates, by Bednorz and Muller. In particular, the pursuit of understanding the mysterious origin of superconductivity in the cuprates and other associated strange phenomena has fascinated the condensed matter community over last two and half decades leading to most of the important unsolved, and probably interconnected, problems of quantum condensed matter physics such as the metal-insulator transition in low dimensions breakdown of Fermi liquid theory, the origin and behavior of unconventional superconductivity, quantum critical points, electronic in homogeneities and localization in interacting systems. This thesis is devoted to the study of some of the aspects of high-temperature superconductivity and associated phenomena in cuprates. In what follows, I give an overview of the organization of the thesis in to different chapters and their contents. For setting up the stage, in Chapter 1, I give a brief account of some of the remarkable phenomena and properties observed in strongly correlated electronic matter and their salient features, that continue to draw much attention and excitement in current times. The peculiarity of the state of affairs in these systems is emphasized and motivated in the background of the paradigmatic Landau Fermi liquid theory and Hubbard model, the minimal model that is expected to capture the quintessence of electronic strong correlation. In Chapter 2, starting with a brief historical account of the discovery of superconductivity in cuprates, the crystal structure of these materials, their chemical realities and basic electronic details are reviewed. This is followed by a survey of the phase diagram of cuprates, doped with, say, x number of holes per copper site, and a plethora of experimental findings that constitute the high-c puzzle. Characteristics of various observed phases, such as the superconducting, pseudo gap and strange metal phases, are discussed on the basis off acts accumulated through various experimental probes, e.g. nuclear magnetic resonance(NMR), neutron scattering, specific heat, transport and optical conductivity measurements as well as photo emission, tunnelling and Raman spectroscopies. As elucidated, these experiments point toward the need for an unconventional mechanism of superconductivity in cuprates and, more so, for the description of the rather abnormal high-temperature normal state that is realized above the superconducting transition temperature c. Keeping in mind the fact that there is no consensus even about the minimal microscopic electronic model, I review two models, namely the three band model and the t - J model; various approximate treatments of these models have dominated the theoretical developments in this field. A large number of theoretical pictures have been proposed based on different microscopic, semi-microscopic and phenomenological approaches in the past two decades for explaining the genesis of the observed strange phenomena in high-c cuprates. I include brief discussions on only a few of them while citing relevant references. As mentioned above, a variety of approximate microscopic theories, based on both strong and weak coupling approaches, as well as numerical techniques have been tried to understand the cuprate phase diagram and capture the aspects of strong correlations in-built in Hubbard and t -J models. On the other hand, in conventional superconductors and, in general, for the study of phase transitions, phenomenological Ginzburg-Landau(GL) functionals written down from very general symmetry grounds have provided useful description for a variety of systems. Specially, Ginzburg-Landau theory has been proven to be complementary to the BCS theory for attacking a plethora of situations in superconductors, e.g., in homogeneities, structures of an isolated vortex and the vortex lattice etc. The GL functional has found wide applicability for the study of vortex matter in high-c superconductors as well. Inspired by the success of this type of phenomenological route, we propose and develop in Chapter 3 an approach, analogous in spirit to that of Ginzburg and Landau, for the superconducting and pseudogap phases of cuprates. We encompass a large number of well known phenomenologies of cuprate superconductivity in the form of a low-energy effective lattice functional of complex spin-singlet pair amplitudes with magnitude Δm and phase m, i.e. m =Δm exp(i m), that resides on the Cu-Cubonds(indexed by m)of the CuO2 planes of cuprates. The functional respects general symmetry requirements, e.g. the -wave symmetry of the superconducting order parameter as found in experiments. The assumptions and the specific physical picture behind such an approach as well as the key empirical inputs that go into it are discussed in this chapter. We calculate the superconducting transition temperature c and the average magnitude of the local pair amplitude, Δ= (Δm), using single-site mean-field theory for the model. We show that this approximation leads to general features of the doping-temperature(x - T )phase diagram in agreement with experiment. In particular, we find a phase coherent superconducting state with d-wave symmetry below a parabolic Tc (x) dome and a phase incoherent state with a perceptible local gap that persists up to a temperature around which can be thought of as a measure of the pseudogap temperature scale T* . Further, effects of thermal fluctuations beyond the mean-field level are captured via Monte Carlo(MC) simulations of the model for a finite two-dimensional (2D) lattice. We exhibit results for Tc obtained from MC simulations as well as that estimated in a cluster mean field approximation. Based on our picture we remark on contrasting scenarios proposed for the doping dependence of the pseudogap temperature. Chapter 4 describes fluctuation phenomena related to pairing degrees of freedom and manifestations of these effects in various quantities of interest, e.g. superfluid density, specific heat etc., at finite temperature. Fluctuation effects have been studied in detail in superconductors over the years and pursued mainly using either the conventional GL functional or the BCS-framework at a microscopic level. However, the picture, in which the pseudogap phase is viewed as one consisting of bond-pairs with a d-wave symmetry correlation length growing as T approaches Tc, implies fluctuation phenomena of quite a different kind, as we discuss here. The contribution of the bond-pair degrees of freedom to thermal properties is obtained here from the lattice free-energy functional using MC simulation, as mentioned in the preceding paragraph. The results for the superfluid density or superfluid stiffness ps, a quantity measured e.g. via the penetration depth, are discussed. As shown, its doping and temperature dependence compare well with experimental results. In this chapter, I also report the calculation of the fluctuation specific heat Cv(T) and find that there are two peaks in its temperature dependence, a sharp one connected with Tc (ordering of the phase of m)and a relatively broad one(hump)connected to T* (rapid growth of the magnitude of Δm). The former is specially sensitive to the presence of a magnetic field, as we find in agreement with experiment. Vortices are relevant excitations in a superconductor and, in particular, in 2D orquasi-2D systems vortices influence the finite temperature properties in a major way. The results for the temperature dependence of vortex density obtained in the MC simulation of the GL-like model are also mentioned in Chapter 4. I report an estimate of the correlation length as well. These results might have relevance for the large Nernst signal observed over a broad temperature range above c in cuprates, as pointed out there. Properties of an isolated vortex and collective effects arising due to interaction between vortices are of much significance for understanding mixed state of type-II superconductors and thus of cuprates. The superconducting order is destroyed in the core region around the centre of a vortex and the vortex core carries signatures of the normal state in a temperature regime where it is generally unattainable due to occurrence of superconductivity. As mentioned in Chapter 5, vortex properties(e.g. electronic excitation spectrum at the vortex core) in BCS superconductors have been explored theoretically, at a microscopic level through the Bogoliubov-deGennes(BdG) theory as well as using the Ginzburg-Landau functional. However, properties of vortices in cuprate superconductors have been found to be much more unusual than could possibly be captured by straightforward extensions of BCS theory to a -wave symmetry case. Chapter 5 briefly reviews the experimental findings on vortices in the superconducting state of cuprates, mainly as probed by Scanning Tunnelling Microscopy(STM) as well as from other probes such as NMR, neutron scattering, SR etc. I discuss some of the consequences of our GL-like functional regarding vortex properties, namely that of the vortex core and the region around it. We use our model to find Δm and m at different sites m for a 2π vortex whose core is at the midpoint of a square plaquette of Cu lattice sites. The vortex is found to change character from being primarily a phase or Josephson vortex for small x to a more BCS-like or Abrikosov vortex with a large diminution in the magnitude Δm as one approaches the vortex core, for large . Here I do not make any direct comparison with experimental data but discuss implications of our results in the background of existing experimental facts. Unravelling the mysteries of high-Tc cuprates should necessarily involve the understanding of electronic excitations over a broad regime of doping and temperature encompassing the pseudo gap, superconducting and strange metal states. A phenomenological theory which aims to describe the pseudo gap phase as one consisting of preformed bond-pairs, is required to include both unpaired electrons and Cooper pairs of the same electrons coexisting and necessarily coupled with each other. In our Ginzburg Landau approach only the latter are explicit, while the former are integrated out. However, effects connected with the pair degrees of freedom are often investigated via their coupling to electrons, one very prominent examples being Angle Resolved Photoemmision Spectroscopy(ARPES),in which the momentum and energy spectrum of electrons ejected from the metal impinged by photons is investigated. In Chapter 6, we develop a unified theory of electronic excitations in the superconducting and pseudo gap phases using a model of electrons quantum mechanically coupled to spatially and temporally fluctuating Cooper pairs(the nearest neighbour singlet bond pairs). We discuss the theory and a number of its predictions which seem to be in good agreement with high resolution ARPES measurements, which have uncovered a number of unusual spectral properties of electrons near the Fermi energy with definite in-plane momenta. We show here that the spectral function of electrons with momentum ranging over the putative Fermi surface(recovered at high temperatures above the pseudogap temperature scale) is strongly affected by their coupling to Cooper pairs. On approaching Tc i.e. the temperature at which the Cooper pair phase stiffness becomes nonzero, the inevitable coupling of electrons with long-wavelength(d-wave symmetry) phase fluctuations leads to the observed characteristic low-energy behavior as reported in Chapter 6. Collective d-wave symmetry superconducting correlations develop among the pairs with a characteristic correlation length ξ which diverges on approaching the continuous transition temperature Tc from above. These correlations have a generic form for distances much larger than the lattice spacing. As we show here, the effect of these correlations on the electrons leads, for example, to a pseudogap in electronic density of states for T > T c persisting till T* , temperature-dependent Fermi arcs i.e. regions on the Fermi surface where the quasiparticle spectral density is non zero for a zero energy excitation and to the filling of the antinodal pseudogap in the manner observed. Further, the observed long-range order(LRO) below c leads to a sharp antinodal spectral feature related to the non zero superfluid density, and thermal pair fluctuations cause a deviation(‘bending’) of the inferred ‘gap’ as a function of k from the expected d-wave form (cos kxa - cos kya). The bending, being of thermal origin, decreases with decreasing temperature, in agreement with recent ARPES measurements. I conclude in Chapter 7 by mentioning some natural directions in which the functional and the approach used here could be taken forward. The phenomenological theory proposed and developed in this thesis reconciles and ties together a range of cuprate superconductivity phenomena qualitatively and confronts them quantitatively with experiment. The results, and their agreement with a large body of experimental findings, strongly support the mechanism based on nearest neighbor Cooper pairs, and emergence of long-range -wave symmetry order as a collective effect arising from short range interaction between these pairs. This probably points to the way in which high-c superconductivity will be understood.

This thesis presents the investigation of magnetism in a selection of low-dimensional systems and its relation to other physical properties, such as superconductivity. The techniques employed are muon spin rotation and pulsed magnetic field magnetisation. The ability of muons to directly probe the local field is used to study SrFeAsF, which is a parent compound of the high-temperature superconducting pnictides. This revealed that the magnetic and structural transitions are separated in this system. I then demon- strate the coexistence of magnetism and superconductivity in NaFeAs for the first time. This discovery is of great interest since the interplay between magnetism and supercon- ductivity is thought to play an important role for high-temperature superconductivity. I further investigate the effect of partially replacing Fe with Co in NaFeAs. I study the ordering and spin reorientation in the Mott insulator Sr₂IrO₄, which has been suggested as a possible high-temperature superconductor. The complex magnetism observed in this system is contrasted to that in related iridates Ca₄IrO₆, Ca₅Ir₃O₁₂ and Sr₃Ir₂O₇. By combining pulsed-field magnetization and low magnetic field experiments with μSR on a series of coordination polymers. I am able to determine the size and direction of the magnetic exchange interaction. I demonstrate how it is possible to adjust the in- teractions by altering the molecular architecture of these Cu-based spin- 1 2 compounds. This is a significant contribution since it will lead to the targeted design of magnetic systems that can be utilized to experimentally test fundamental theories of magnetism.

Inwardly rectifying potassium (Kir) channels are essential for controlling the excitability of eukaryotic cells, forming a key part of the inter-cellular signalling system in multi-cellular organisms. However, as prokaryotic (KirBac) channels are less technically challenging to study in vitro and have been shown to be directly homologous to eukaryotic channels, they are often studied in lieu of their mammalian counterparts. A vital feature of Kir and KirBac channels is their mechanism for opening and closing, or their gating: this study predominantly features observations of open and/or closed channel populations. A well-characterised member of the KirBac family, KirBac1.1, has been successfully expressed, purified into detergent micelles, and doubly labelled with fluorescent maleimide dyes in order to enable observation of confocal-in-solution Förster Resonance Energy Transfer (FRET) at the single molecule level. Results demonstrate single-molecule FRET signals from KirBac1.1 and therefore represent the first single-molecule FRET observations from a KirBac channel. Perturbation of the open-closed dynamic equilibrium was performed via activatory point mutations, changes in pH, and ligand binding. A protocol for reconstitution into nanodiscs was optimised in order to more closely approximate native conditions, and the single-molecule FRET observations repeated. This thesis presents a comparison between measurements made using the detergent solubilisation system and those made using nanodiscs.

Molecular dynamics (MD) simulations are used to compute the equilibrium dynamics of a single component fluid with Yukawa interaction potential v(r) = (Ze)^2 exp(−r/λs )/4π eps_0 r. This system, which is known as the Yukawa one-component plasma (YOCP), represents a simplified description of a non-ideal plasma consisting of ions, charge Ze, and electrons. For finite screening lengths λs, the MD results are used to investigate the domain of validity of the hydrodynamic description, i.e., the description given by the Navier-Stokes equations. The way in which this domain depends on the thermodynamic conditions of the YOCP, as well as the strength and range of the interactions, is determined. Remarkably, it is found that the domain of validity is completely determined by the range of the interactions (i.e., λs); this alone determines the maximum wave number k_max at which the hydrodynamic description is applicable. The dynamics of the YOCP at wavevectors beyond k_max are then investigated; these are shown to be in striking agreement with a simple and well known generalisation of the Navier-Stokes equations. In the extreme case of the Coulomb interaction potential (λs = ∞), the very existence of a hydrodynamic description is a known but unsolved problem [Baus & Hansen, 1980]. For this important special case, known as the one-component plasma (OCP), it is shown that the ordinary hydrodynamic description is never valid. Since the OCP is the prototypical system representing a non-ideal plasma, a number of different approaches for modelling its dynamics have been formulated previously. By computing the relevant quantities with MD, the applicability of a number of models proposed in the literature is examined for the first time.

Organic photovoltaics have attracted considerable research and commercial interest due to their lightness, mechanical flexibility and low production costs. There are two main approaches for the fabrication of organic solar cells – solution and vacuum processing. The former relies on morphology control in polymer-fullerene blends resulting from natural phase separation in these systems. The latter takes advantage of solvent-free processing allowing highly complex multi-junction architectures similar to inorganic solar cells. This work aims to combine the benefits of both by depositing conjugated polymers using vacuum thermal evaporation. By employing this unconventional approach it aims to enhance the efficiency of organic photovoltaics through increased complexity of the thin-film architecture while improving the nanoscale morphology control of the individual active layers. The thesis explores the vacuum thermal deposition of polythiophenes, mainly poly(3-hexylthiophene) (P3HT) and side-group free poly(thiophene) (PTh). A variety of chemical techniques, such as NMR, FT-IR, GPC, DSC and TGA, are used to examine the effect of heating on chemical structure of the polymers. Optimal processing parameters are identified and related to the resulting thin-film morphology and charge transport properties. Efficient photovoltaic devices based on polythiophene donors and fullerene acceptors are fabricated. Materials science techniques AFM, XRD, SEM, TEM and MicroXAM are used to characterize topography and morphology of the thin films, and UV-Vis, EQE, I-V and C-V measurements relate these to the optical and electronic properties. The results of the study show that polymer side groups have a strong influence on molecular packing and charge extraction in vacuum-deposited polymer thin films. Unlike P3HT, evaporated PTh forms highly crystalline films. This leads to enhanced charge transport properties with hole mobility two orders of magnitude higher than that in P3HT. The effect of molecular order is demonstrated on polymer/fullerene planar heterojunction solar cells. PTh-based devices have significantly better current and recombination characteristics, resulting in improved overall power conversion efficiency (PCE) by 70% as compared to P3HT. This confirms that the chemical structure of the molecule is a crucial parameter in deposition of large organic semiconductors. It is also the first-ever example of vacuum-deposited polymer photovoltaic cell. Next, vacuum co-deposited PTh:C60 bulk heterojunctions with different donor-acceptor compositions are fabricated, and the effect of post-production thermal annealing on their photovoltaic performance and morphology is studied. Co-deposition of blended mixtures leads to 60% higher photocurrents than in thickness-optimized PTh/C60 planar heterojunction counterparts. Furthermore, by annealing the devices post-situ the PCE is improved by as much as 80%, achieving performance comparable to previously reported polythiophene and oligothiophene equivalents processed in solution and vacuum, respectively. The enhanced photo-response is a result of favourable morphological development of PTh upon annealing. In contrast to standard vacuum-processed molecular blends, annealing-induced phase separation in PTh:C60 does not lead to the formation of coarse morphology but rather to an incremental improvement of the already established interpenetrated nanoscale network. The morphological response of the evaporated PTh within the blend is further verified to positively differ from that of its small-molecule counterpart sexithiophene. This illustrates the morphological advantage of polymer-fullerene combination over all other vacuum-processable material systems. In conclusion, this processing approach outlines the conceptual path towards the most beneficial combination of solution/polymer- and vacuum-based photovoltaics. It opens up a fabrication method with considerable potential to enhance the efficiency of large-scale organic solar cells production.

Spectroscopic measurements are detailed within this thesis, utilising incoherent neutron scattering to examine the dynamics of various condensed-matter systems, from nanosecond to sub-femtosecond timescales. The body of this work is divided into two distinct areas of research. I. Nuclear Momentum Measurements of Multiple Masses Deep inelastic neutron scattering (DINS) is used to probe the nuclear momentum distributions and kinetic energies of individual atomic species in sodium hydride (both in bulk and as nanoparticulates within a silica matrix), enriched lithium-7 fluoride and lithium tetra-ammoniate. Extension of DINS to examine heavier (M>4amu) nuclei is detailed, accomplished by the application of a simple stoichiometric fixing technique within the standard DINS theory and analysis protocols. The validity and accuracy of such simultaneous measurements are discussed. II. The Dynamics of Coordinated Ammonia in Zeolite A Inelastic neutron scattering (INS) and quasielastic neutron scattering (QENS) are utilised in the examination of vibrational and stochastic dynamics of the ammonia molecule, as coordinated to the internal surface of a zeolite host. Both sodium and copper-exchanged forms of zeolite-A are studied, with proton-weighted, low energy phonon-modes and rotational processes being observed and assigned.

The design, construction and characterisation of a novel, arrayed, open-access optical microcavity is described. Included in this thesis are the precise fabrication details, making use of the focused ion beam. A technique for analysing and optimising the microcavities constructed, making use of an atomic force microscope is also included. Results from the optical characterisation of the fabricated microcavities are presented, including quality factors of around 104, and fitnesses of around 400. The optical analysis then progressed onto coupling colloidal semiconductor nanocrystals to the microcavity modes. This yielded room temperature Purcell enhancements, single particle sensing, and also allowed for the characterisation of a second iteration of cavities. This improved set was shown to achieve fitnesses in excess of 1800 and quality factors with a lower limit of 15000. The optical identification of single NV centres in nanodiamond is discussed, along with the development of an optical apparatus to couple them to microcavities at cryogenic temperatures. Finally several results from finite difference time domain simulations will be presented, showing ultimate mode volumes of less than 0.5 cubic wavelengths are possible for this approach.

Dye-sensitized solar cells (DSSCs) and perovskite solar cells are emerging as promising potential low-cost alternatives to established crystalline silicon photovoltaics. Of the employed functional materials, however, many fundamental optoelectronic properties governing photovoltaic device operation are not sufficiently well understood. This thesis reports on a series of studies using ultrafast THz and photoluminescence spectroscopy on two classes of such materials, providing insight into the dynamics of charge-transport and recombination processes following photoexcitation. For TiO₂-nanotubes, which have been proposed as easy-to-fabricate electron transporters for DSSCs, fast, shallow electron trapping is identified as a limiting factor for efficient charge collection. Trapping lifetimes are found to be about an order of magnitude shorter than in the prevalently employed sintered nanoparticles under similar excitation conditions and trap saturation effects are not observed, even at very high excitation densities. In organo-lead halide perovskites - specifically CH₃NH₃PbI₃ and CH₃NH₃PbI_3-xCl_x, which have only recently emerged as highly efficient absorbers and charge transporters for thin-film solar cells, carrier mobilities and fundamental recombination dynamics are revealed. Extremely low bi-molecular recombination rates at least four orders of magnitude below the prediction of Langevin's model are found as well as relatively high charge-carrier mobilities in comparison to other solution-processable materials. Furthermore a very low influence of trap-mediated recombination channels was observed. Due to a combination of these factors, diffusion lengths reach hundreds of nanometres for CH₃NH₃PbI₃ and several microns for CH₃NH₃PbI_3-xCl_x. These results are shown to hold for both, solution processed and vapour-deposited CH₃NH₃PbI_3-xCl_x and underline the superb suitability of the materials as absorbers in solar cells, even in planar heterojunction architectures. The THz-frequency spectrum of the conductivity of the investigated perovskites is consistent with Drude-like charge transport additionally exhibiting weak signatures of phonon coupling. These coupling effects are also reflected in the luminescence of CH₃NH₃PbI_3-xCl_x, where they are believed to be the cause of the observed homogeneous spectral broadening. Further photoluminescence measurements were performed at temperatures between 4 K and room temperature to study the nature of recombination pathways in the material.

In this thesis, the response of DNA and RNA to linear and torsional mechanical stress is studied using coarse-grained models. Inspired by single-molecule assays developed over the last two decades, the end-to-end extension, buckling and torque response behaviour of the stressed molecules is probed under conditions similar to experimentally used setups. Direct comparison with experimental data yields excellent agreement for many conditions. Results from coarse-grained simulations are also compared to the predictions of continuum models of linear polymer elasticity. A state diagram for supercoiled DNA as a function of twist and tension is determined. A novel confomational state of mechanically stressed DNA is proposed, consisting of a plectonemic structure with a denaturation bubble localized in its end-loop. The interconversion between this novel state and other, known structural motifs of supercoiled DNA is studied in detail. In particular, the influence of sequence properties on the novel state is investigated. Several possible implications for supercoiled DNA structures in vivo are discussed. Furthermore, the dynamical consequences of coupled denaturation and writhing are studied, and used to explain observations from recent single molecule experiments of DNA strand dynamics. Finally, the denaturation behaviour, topology and dynamics of short DNA minicircles is studies using coarse-grained simulations. Long-range interactions in the denaturation behaviour of the system are observed. These are induced by the topology of the system, and are consistent with results from recent molecular imaging studies. The results from coarse-grained simulations are related to modelling of the same system in all-atom simulations and a local denaturation model of DNA, yielding insight into the applicability of these different modelling approaches to study different processes in nucleic acids.